Inside, the chapel's simple elegant hall has the pale colors, flat ceiling and cut glass chandeliers reminiscent of contemporary domestic interiors. In contrast to the awe-inspiring[opinion] interior of Trinity Church, this hall and its ample gallery were endowed with a cozy and comfortable character in order to encourage attendance.

On the Broadway side of the chapel's exterior is an oak statue of the church's namesake, Saint Paul, carved in the American Primitive style. Below the east window is the monument to Brigadier General Richard Montgomery, who died at the Battle of Quebec (1775) during the American Revolutionary War. In the spire, the first bell is inscribed "Mears London, Fecit [Made] 1797." The second bell, made in 1866, was added in celebration of the chapel's 100th anniversary.

The Hearts of Oak, a militia unit organized early in the American Revolutionary War, and comprised in part of King's College (later, Columbia University) students, would drill in the Chapel's yard before classes nearby. Alexander Hamilton was an officer of this unit.

For eight months, hundreds of volunteers worked 12-hour shifts around the clock, serving meals, making beds, counseling and praying with fire fighters, construction workers, police and others. Massage therapists, chiropractors, podiatrists and musicians also tended to their needs.

The church survived without even a broken window. Church history declares it was spared by a miracle sycamore on the northwest corner of the property that was hit by debris. The tree's root has been preserved in a bronze memorial by sculptor Steve Tobin. While the church's organ was badly damaged by smoke and dirt, the organ has been refurbished and is in use again.[7]

The fence around the church grounds became the main spot for visitors to place impromptu memorials to the event. After it became filled with flowers, photos, teddy bears, and other paraphernalia, chapel officials decided to erect a number of panels on which visitors could add to the memorial. Estimating that only 15 would be needed in total, they eventually required 400.

Rudolph Giuliani gave his mayoral farewell speech at the church on December 27, 2001.

The Chapel is now a popular tourist destination since it still keeps many of the memorial banners around the sanctuary and has an extensive audio video history of the event. There are a number of exhibits in the Chapel. The first one when entering is "Healing Hearts and Minds", which consists of a policeman's uniform covered with police and firefighter patches sent from all over the country, including Iowa, West Virginia, California, etc. The most visible is the "Thread Project", which consists of several banners, each of a different color, and woven from different locations from around the globe, hung from the upper level over the pews.

The chapel has hosted many famous worshippers. George Washington worshiped here on his Inauguration Day, April 30, 1789. During the two years New York City was the country's capital, Washington attended services at St. Paul's while Trinity Church was being rebuilt. Hanging above Washington's pew is a painting of the Great Seal of the United States (adopted in 1782), which was commissioned by the Vestry in 1785. The artist of the painting is unknown.